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<!doctype html>
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<h1>OHSU Big Data to Knowledge (BD2K)</h1>
<h2>Open Educational Resources (OERs) Project</h2>
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<nav>
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="topics.html">Modules</a></li>
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Welcome to our beta site and modules! This website and the modules are under development and we welcome any feedback on this website and on the individual modules.
</section>
<header>
<h1>Modules</h1>
<p>A list of modules developed for the project are listed here. The first group of modules are the completed courses. The second group of modules are still in development.</p>
<p>All of the completed modules are also available in our <a href='https://github.com/OHSUBD2K/' target='_BLANK'>github repository</a> <img src="img/github.png" alt="github octocat silhouette"/></p>
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<section class="ready">
<h2>Available Modules</h2>
<p>Clicking on the title of module will present a brief overview of the module. Below the overview, clicking on the "view" button will allow you to see the various parts of the module, sample the modules, or download pieces of the topic. </p>
<div class="listoftopics">
<ul>
<li>
<div class="topicTitle">
<a href="BDK01.html">Biomedical Big Data Science</a>
</div>
<div class="topicID">
BDK01
</div>
<div class="topicDescription">
Overview of biomedical big data science and biomedical, clinical, and translational research.
</div>
<div class="seClear"></div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK02.html">Introduction to Big Data in Biology and Medicine</a>
</div>
<div class="topicID">
BDK02
</div>
<div class="topicDescription">
Examples of issues of measurement and scale; avoid “big data hubris” with examples from Google Flu Trends
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK03.html">Ethical Issues in Use of Big Data</a>
</div>
<div class="topicID">
BDK03
</div>
<div class="topicDescription">
Discussion of the major ethical issues surrounding the use of data
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK04.html">Clinical Data Standards Related to Big Data</a>
</div>
<div class="topicID">
BDK04
</div>
<div class="topicDescription">
Overview of clinical data standards related to big data.
</div>
<div class="seClear"></div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK05.html">Basic Research Data Standards</a>
</div>
<div class="topicID">
BDK05
</div>
<div class="topicDescription">
Standards for biomedical data, participating in communities that develop them, aiding reproducibility
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK06.html">Public Health and Big Data</a>
</div>
<div class="topicID">
BDK06
</div>
<div class="topicDescription">
Overview of public health and its use of big data
</div>
<div class="seClear"></div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK07.html">Team Science</a>
</div>
<div class="topicID">
BDK07
</div>
<div class="topicDescription">
“Team Science” will define team science in the context of modern bioinformatics research. The module will highlight some of the most pressing considerations facing team science, and provide a basic framework for understanding and establishing high functioning teams.
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK08.html">Secondary Use (Reuse) of Clinical Data</a>
</div>
<div class="topicID">
BDK08
</div>
<div class="topicDescription">
Overview of the secondary use (or re-use) of clinical data
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK09.html">Publication and Peer Review</a>
</div>
<div class="topicID">
BDK09
</div>
<div class="topicDescription">
Overview of the process of publication of scientific data and information, including peer review, journal literature, and limitations of the scientific literature
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK10.html">Information Retrieval</a>
</div>
<div class="topicID">
BDK10
</div>
<div class="topicDescription">
Overview of information retrieval (search) for knowledge-based information.
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK12.html">Data annotation and curation</a>
</div>
<div class="topicID">
BDK12
</div>
<div class="topicDescription">
Data preparation, developing standardized quality assurance processes and pipelines
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK14.html">Ontologies 101</a>
</div>
<div class="topicID">
BDK14
</div>
<div class="topicDescription">
Introduction to OWL2 and data reasoning
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK15.html">Data metadata and provenance</a>
</div>
<div class="topicID">
BDK15
</div>
<div class="topicDescription">
Data set descriptions, ISA-TAB, and W3C standards for versioning, provenance, and attribution
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK16.html">Semantic data Interoperability</a>
</div>
<div class="topicID">
BDK16
</div>
<div class="topicDescription">
Tools to semantically integrate data
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK17.html">Choice of Algorithms and Algorithm Dynamics</a>
</div>
<div class="topicID">
BDK17
</div>
<div class="topicDescription">
Current approaches for modeling and mining Big Data; Streaming and parallel algorithms; Optimization considerations
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK18.html">Visualization and Interpretation</a>
</div>
<div class="topicID">
BDK18
</div>
<div class="topicDescription">
Streaming data visualization; Visual data mining; Visual search and recommendation; Big data storytelling using visualization; Scalable parallel visualization methods; Advanced hardware and architecture for data visualization and analysis; Human computer interaction
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK19.html">Replication, Validation and the spectrum of Reproducibility</a>
</div>
<div class="topicID">
BDK19
</div>
<div class="topicDescription">
The spectrum of reproducibility; Replication vs. Validation; Data Integrity
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK20.html">Regulatory Issues in Big Data for Genomics and Health</a>
</div>
<div class="topicID">
BDK20
</div>
<div class="topicDescription">
Research regulations; Privacy regulations; Compliance
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK21.html">Hosting data dissemination and data stewardship workshops</a>
</div>
<div class="topicID">
BDK21
</div>
<div class="topicDescription">
Workshop materials and documentation for leading workshops pertaining to NIH guidelines, best practices for data management, data standards, data linking, public repositories, and your scholarly footprint
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
<li>
<div class="topicTitle">
<a href="BDK22.html">Guidelines for Reporting, Publications, and Data Sharing</a>
</div>
<div class="topicID">
BDK22
</div>
<div class="topicDescription">
Review of current policies and how they pertain to different organizations; Data sharing versus data reuse; being a good big data reviewer
</div>
<div class="seClear">
</div>
<div class="topic_details">
<div class="topic_info_placement"></div>
</div>
</li>
</ul>
</div>
</section>
<section class="stillDev">
<h2>Still Under Development</h2>
<p> These modules have yet to be finalized, but will be soon made available.</p>
<div class="listoftopics">
<ul>
<li>
<div class="topicTitle">
Version control and identifiers
</div>
<div class="topicID">
BDK11
</div>
<div class="topicDescription">
How to apply quality data management principles in both private and public venues
</div>
<div class="seClear">
</div>
</li>
<li>
<div class="topicTitle">
Data and tools landscape
</div>
<div class="topicID">
BDK13
</div>
<div class="topicDescription">
Where to find and access data, vocabularies, and software tools
</div>
<div class="seClear">
</div>
</li>
<li>
<div class="topicTitle">
Terminology of Biomedical, Clinical, and Translational Research
</div>
<div class="topicID">
BDK23
</div>
<div class="topicDescription">
Review of the various terms used in Big Data and related areas
</div>
<div class="seClear">
</div>
</li>
<li>
<div class="topicTitle">
Computing Concepts for Big Data
</div>
<div class="topicID">
BDK24
</div>
<div class="topicDescription">
Overview of computing issues arising in the presence of large and/or distributed data
</div>
<div class="seClear">
</div>
</li>
<li>
<div class="topicTitle">
Data modeling
</div>
<div class="topicID">
BDK25
</div>
<div class="topicDescription">
Use of modeling tools to plan data representation
</div>
<div class="seClear">
</div>
</li>
<li>
<div class="topicTitle">
Semantic Web data
</div>
<div class="topicID">
BDK26
</div>
<div class="topicDescription">
Accessing, integrating, and publishing data in RDF triplestores, SPARQL querying
</div>
<div class="seClear">
</div>
</li>
<li>
<div class="topicTitle">
Context-based selection of data
</div>
<div class="topicID">
BDK27
</div>
<div class="topicDescription">
Determining when to use Big Data; Experimental Design considerations for Big Data
</div>
<div class="seClear">
</div>
</li>
<li>
<div class="topicTitle">
Translating the Question
</div>
<div class="topicID">
BDK28
</div>
<div class="topicDescription">
Translating your question to a testable hypothesis leveraging Big Data
</div>
<div class="seClear">
</div>
</li>
<li>
<div class="topicTitle">
Implications of Provenance and Pre-processing
</div>
<div class="topicID">
BDK29
</div>
<div class="topicDescription">
Determining Lineage and Provenance in Big Data; Impact of pre-processing on downstream-analysis;
</div>
<div class="seClear">
</div>
</li>
<li>
<div class="topicTitle">
Data tells a story
</div>
<div class="topicID">
BDK30
</div>
<div class="topicDescription">
Exploratory data analysis; Data Cleaning
</div>
<div class="seClear">
</div>
</li>
<li>
<div class="topicTitle">
Statistical Significance, P-hacking and Multiple-testing
</div>
<div class="topicID">
BDK31
</div>
<div class="topicDescription">
Determining Statistical Significance in the context of your hypothesis; Effect size and confidence intervals; Dangers of “p-hacking”; Multiple testing considerations
</div>
<div class="seClear">
</div>
</li>
<li>
<div class="topicTitle">
Displaying Confidence and Uncertainty
</div>
<div class="topicID">
BDK32
</div>
<div class="topicDescription">
Review of “Big Uncertain Data”; Quantifying uncertainty; Probabilistic databases; Incorporation in decision aid modeling
</div>
<div class="seClear">
</div>
</li>
</ul>
</div>
</section>
</article>
<aside>
<h3>Feedback</h3>
<p>Your feedback is welcome!</p>
<p>The modules and this site are in the development phase and we value your feedback to help improve these educational materials.</p>
<a href="https://www.surveymonkey.com/r/BD2K-OER-Feedback" target="_BLANK">Module Feedback and Evaluation Form</a>
</aside>
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<h3>Funding</h3>
<p>These materials are supported by the National Institute of General Medical Sciences, funded by the NIH Big Data to Knowledge Initiative, under Award Number <a href="http://projectreporter.nih.gov/project_info_description.cfm?aid=8828784&icde=22004384" target="_BLANK">1R25GM114820</a>.</p>
</div>
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<h3>Contact Us</h3>
<p><a href="http://goo.gl/forms/kBdoFsLXeW" target="_BLANK">Contact Form</a></p>
<ul>
<li>BD2K OHSU Open Educational Resources Project</li>
<li>Oregon Health & Science University</li>
<li>Mail Code: BICC</li>
<li>3181 S.W. Sam Jackson Park Rd.</li>
<li>Portland, OR 97239-3098</li>
</ul>
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